|Course coordinator(s)||dr. FT Bakker|
|Lecturer(s)||dr. FT Bakker|
|dr. S Simon|
|Examiner(s)||dr. FT Bakker|
Language of instruction:
Assumed knowledge on:
Basic concepts in systematics, as treated in Evolution and Systematics (GEN-11306). (MSc) students from outside WU should contact the course coordinator and plan an intake session, preparing to catch up with the book chapters used in GEN-11306.
Many questions in biology need an evolutionary or phylogenetic perspective, for instance to distinguish convergent evolution from independent, divergent, evolution. This course focuses on the analysis of comparative data, at and above the species level, enabling such questions to be addressed, as well as on obtaining a better understanding of species diversity and phylogenetic relationships. Apart from core systematics (i.e. taxonomy, phylogeny and speciation/domestication studies), the course also offers a perspective on molecular evolution and how it's processes and patterns are used in the reconstruction of species relationships both in space (biogeography) and time (millions of years, molecular dating). You will also learn how to optimize morphological or ecological data onto DNA-based phylogenetic trees, estimating ancestral states. The course offers hands-on analytical experience, and confronts the students with current literature.
In the first week the basic concepts of systematics (including taxonomy) will be treated to bring you all up to speed, and make sure we are at the same level. In principle, the material offered here pre-supposes you have successfully completed the course Evolution & Systematics (GEN-11306), or have a comparable background knowledge. Concepts treated are: the field of systematics, species, taxonomy & nomenclature, characters, homology & DNA barcoding, and comparative analysis & morphometrics.
In week 2 In this week we will focus on phylogenetics and how to sample, compile & analyse DNA and protein sequence data in order to build phylogenetic trees. You will be using optimality criteria such as likelihood and posterior probability in order to find best possible trees, as well as conduct distance analyses. We will be using DNA and protein sequence data sets for genes (both separate, and in concert) of different main plant clades (Angiosperms, Land plants, Rosids, Asterids, etc.). Whereas normally no ‘true trees’ are available, in this case we will use the APG tree as such, as it is corroborated maximally by other evidence and can therefore be considered a true tree during this practical. This enables comparing the relative performance of the various methods and optimality criteria used in phylogeny estimation.
In week 3 the focus will shift from tree-building to tree-interpretation, i.e. once I have a (sample of) tree(s) what can I do with it? You will compare your results across parsimony, likelihood and Bayesian analyses in terms of clades and their support and document this in your Phylogeny Workbook. You will also be focussing on analysing the output from a Markov Chain (used in Bayesian analysis), and perform network reconstruction. Thursday and Friday will be spent on interpreting and presenting on previously published phylogenetic studies in which phylogenetics is prominent.
Currently, phylogenetics is scaling up in terms of character sampling, due to the ever-increasing speed, power and cost-effectiveness with which genomic data can be generated. For phylogenetics this has meant that the number of gene (exon) sequences that phylogenetic trees are based on has scaled-up enormously. In the Week 4 practical you will be working with genomic data generated for insect phylogenetic studies. You will explore insect transcriptome data sets and use concatenated gene sequence alignments that have been compiled for this practical and that will differ in both taxon and character sampling.
In order to truly understand systematic patterns, form, time ánd space must be taken into account. Therefore in this week we will focus on the spatio-temporal dimension to systematics: biogeography and biodiversity assessment, and molecular dating: can we estimate node ages (in millions of years) on our phylogenetic trees?
After successful completion of this course students are expected to be able to:
- explain the current state of systematic research, its challenges and possibilities;
- apply principles of plant and animal nomenclature;
- critically discuss the relevance of the most important species concepts in systematics;
- explain the practice and application of DNA barcoding;
- apply principles & methods used in comparative geometric morphometrics;
- design and execute a phylogenetic reconstruction + interpretation based on aligned DNA and protein sequences, using both distance and maximum likelihood and Bayesian statistical approaches;
- apply principles & methods used in network construction;
- apply principles & methods used in phylogenomics;
- apply principles & methods used in spatio-temporal analysis of biodiversity, i.e. historical biogeographic reconstruction and molecular dating.
These include lectures, guided group-exercises and discussions, and the presentation of scientific papers, prepared by the students in groups of up to three. The phylogeny reconstruction practical includes hands-on exercises and lectures explaining the theoretical and philosophical background of the methods and criteria applied. Results are deposited in a 'Phylogeny Workbook'. In week 5 and 6, the students choose from several modules to conduct a mini-research project focusing on the analysis of comparative data, usually stemming from ongoing research projects elsewhere in and around the Plant Sciences Group community.
- a written exam (open questions) with a minimally required score of 5 (50%);
- assessment of the presentations of scientific papers (5%);
- results of modules of week 5 and 6 (25%);
- assessment of the 'phylogeny workbook' portfolio, incorporating the results of the various phylogenetic analyses (20%).
A printed commands/protocol reference will be made available at the start of the course, and use of the accompanying BlackBoard is essential for further reading, data sets and software, and weblinks to on-line analysis facilities.